Enables slow growth after depletion of glucose
Consistent upregulation observed in: * Sugar utilization pathways (glycolysis, pyruvate utilization) * Butyrate-producing pathways
Source: Liu, B., Garza, D.R., Gonze, D. et al. (2023).
Starvation responses impact interaction dynamics of human gut bacteria…
ISME Journal 17. DOI: 10.1038/…
Fermentation
RNA expression data
Annotation for expression dataset
Meta-data for fermentation dataset
Removing empty time-points from fermentation dataset
Subsetting RNA expression to wild type R. intestinalis only
ri_expression_data |>
pivot_longer(cols = -X,
names_to = "sample",
values_to = "expression") |>
inner_join(ri_metadata, by = c("sample" = "GC.code" )) |>
filter(Exp == "RI_batch_WC") |>
select(X,expression,sample) |>
pivot_wider(names_from = sample,
values_from = expression) |>
write_csv("../data/02_data_clean.csv")